Predicting active siRNAs: explainable models uncover underlying mechanisms

Our results-driven world pressures us to give up good science.

Our results-driven world pressures us to dangerously cut corners. The use of black-box AI in drug R&D is a prime example of this. The underlying problem is simple: we have become so wrapped up in the race to make the most accurate predictions — of effective molecules, of disease biomarkers, of toxicity, of side effects, the list goes on — that we are willing to give up understanding how these predictions arise. In doing so, we give up good science.

Why does the use of black-box AI force us to give up trying to understand the underlying mechanisms hidden in data? It’s due to an inherent characteristic: while good at making predictions, black-box-generated models are uninterpretable to us. Black-box generated models don’t tell us what mechanisms or relationships between features in our data are interacting to make these predictions. This means we are’t learning anything about our data. This stunts scientific discovery.

If we want good science in AI-driven drug development, or any other kind of research for that matter, we need to reemphasize developing our understanding of underlying mechanisms as we make predictions. So let’s reposition ourselves.

It’s not about asking ourselves “How good can we get at predicting”, but rather “What is the best way to interpret what is going on here?”. In doing so we get back to the core values of science and avoid the pitfalls of blind acceptance.

AI with explainability

So if black-box AI is not a suitable tool for this type of mindset, what is? Here we turn to the QLattice — an explainable AI that produces mathematical models that show how specific features interact to predict the target. The QLattice gives us explanations with predictions. Analyzing these explanations helps us understand what’s really going on in the data.

Using explainable models to gain knowledge about siRNA activity

Gene inhibition in RNA therapeutics

Let’s apply our repositioned selves and the QLattice in a very hot area of research: nucleic acid-based medicines. One particular type, RNA interference (RNAi) involves a process by which specific mRNAs are targeted and degraded. Taking advantage of naturally occurring degradation mechanisms allows us to inhibit the expression of specific genes. As you can imagine, this is an interesting drug mechanism for many diseases and disorders ranging from cancer treatments to the mediation of genetic disorders.

There are a few RNA types with slightly different mechanisms to accomplish RNAi, however, here we will focus on the siRNA approach.

The siRNA mechanism

siRNAs, or short interfering RNAs, are double-stranded oligonucleotides of around 20–30 base pairs. Together, the two strands form a duplex consisting of a passenger and guide strand. The guide strand of the siRNAs combine into the RNA-induced silencing complex (RISC) and guides the complex to the mRNA via complementary base pairing. RISC can then degrade the target mRNA preventing its translation into disordered or undesirable proteins.

siRNA mediated mRNA degradation mechanism via RISC
siRNA mediated mRNA degradation mechanism via RISC.

An siRNA is much shorter than its mRNA target. Therefore there are many different siRNA “candidates” for the same target.

Example of siRNA “candidates” tiling the mRNA target
Example of siRNA “candidates” tiling the mRNA target.

However, not all of these siRNAs induce gene silencing, or minimal expression of the undesirable gene. In other words, while a group of different siRNA candidates target the same mRNA, not all are actually effective at inhibiting it’s expression. We can then ask ourselves: are there specific characteristics or features of a given siRNA that can predict its gene silencing potency? Furthermore, how do these features of interest interact to create a mechanism for determining effective siRNAs? We will use the QLattice to answer these questions.

The data

We will use data published by Shabalina et. al. (2006). This dataset includes siRNAs targeting 52 different mRNAs with at least 5 different siRNA per target. Each entry in the data includes some information about the target mRNA, the siRNA sequence, composition and thermodynamic characteristics of the oligonucleotide, and the associated siRNA activity.

siRNA data set

Pre-processing

While the dataset has activity data, these values are numerical. However, we will analyze siRNA activity as a classification problem: we want to predict active versus inactive siRNA, not their specific mRNA inhibition values. This is because there can be various target or assay specific features that impact the measured activity. These would be a big hurdle to overcome if we were to analyze and predict the specific activity values in a regression problem. Furthermore, Shabalina et. al. also performed a classification.

In order to perform this analysis, we first classify each siRNA as active, inactive, or neither according to the method described in the paper. If mRNA expression is at 30% or less after the siRNA treatment, i.e. the RNA expression is inhibited by 70% or more, then the siRNA is considered active. Conversely, if the RNA expression is 70% or more after the siRNA is introduced, i.e. the RNA expression is inhibited by 30% or less, then the siRNA is considered inactive. We will add a column called ‘Class’ to the data. In this column active siRNAs will be denoted with a 1 and inactive with a 0. siRNAs that exhibit between 30% and 70% silencing capabilities will be considered as too ambiguous to be classified. We will drop these.

Finding a model using the QLattice

Abzu QLattice model

In the associated paper, Shabalina et. al. used neural networks to identify the four most powerful predictive features of siRNA activity. They identified Cons_Sum, Content-, Hyb19, and Dif_5–3 as being the four “best” parameters out of the total 18.

Interestingly, we see three of these features in our model. Let’s analyze its performance.

Understanding the features

The QLattice has identified three important features and a simple interaction between them, but what do these features mean?

Cons_Sum

This is a compositional feature and is a numerical representation of which position-nucleotide combinations are preferred and avoided. In other words, at specific base locations active siRNAs may typically have specific nucleotides (a preferred combination) or typically not have specific nucleotides (an avoided combination). Cons_Sum is calculated by subtracting the number of preferred — avoided nucleotides.

Dif_5–3

This is a thermodynamic feature that measures the difference in free energy of the sense-antisense strands of the siRNA. It takes the binding energy (∆G) at the 3'-end minus the binding energy at the 5'-end.

Hyb19

This feature describes the frequency of potential targets for an siRNA along the target mRNA.

Adding more descriptive features

As we saw, Cons_Sum is a summary describing avoided and preferred nucleotides at specific positions in the nucleotide sequence of the guide strand. What specific nucleotides these are, whether they are avoided or preferred, and whether the preference is stronger at specific positions, are important questions whose answers are lost in this attempt to represent these preferences with one summarizing value. The QLattice, however, can handle a combination of numerical and categorical data. This allows us to pass categorical descriptors of the nucleotides present at each position of the siRNA. The QLattice will then point us to important positions in the guide strand where specific nucleotides are avoided or preferred and tell us what these are.

To perform this analysis we’ll need a bigger dataset. We’ll take the one used by Ichihara et. al. (2007). This includes the oligonucleotides analyzed by Shabalina and colleagues, as well as others from other researchers. We’ll add the positional features and Dif_5–3 ourselves.

Classifying the sequences

Ichihara and colleagues performed a regression analysis on the data and don’t give us thresholds for determining active, inactive, and ambiguous siRNAs. With no guide, we’ll have to set them ourselves. Looking at the distribution of inhibition values it would make sense to consider active siRNA as those with an inhibition greater than 80% and inactive as those with inhibition less than 50%. Note that the ‘% Inhibition’ column represents how much the RNA expression was inhibited, with a higher value indicating a more active siRNA (the opposite of what we saw with ‘Activity’ in the Shabalina et. al. dataset).

Abzu chart of inhibition values

Train/test split & data preprocessing

The researchers tell us which siRNAs they included in their train (A1600) and test (A831) sets. We’ll use the same train/test split and call the datasets dataA and dataA2 respectively.

Test split and data preprocessing

Declare the type of input data

We touched on this earlier, but the QLattice can work with a combination of categorical, numerical, and boolean data. However, it automatically assumes the data being passed is numerical, so we have to specify that the positional features we’ve added are actually categorical. The type of input data is called its semantic type and we’ll keep track of the columns we identify as containing categorical type data in a dictionary called ‘stypes_pos’.

Using the QLattice

Now we are ready to generate a model.

Abzu QLattice model

We see that the nucleotide at position 1 has been identified as an important feature when determining active siRNAs. We also see Dif_5–3 has appeared in our model again.

Evaluate performance

Abzu QLattice model

Nucleotide preferences from weights of categoricals

The positive value above the pos1 node shows that position 1 is positively correlated with the output. Therefore the largest positive categorical weight will tell us the most preferred nucleotide.

Nucleotide preferences from weights of categoricals

We see that at position 1 U is most preferred, followed by A, then G and C as (relatively) equally the least favorable.

Model response to Dif_5–3

Abzu QLattice plot
The plot depicts the predicted ‘Class’ of an siRNA according to its Dif_5–3 value (at a constant Whole DG value and pos1 nucleotide ‘U’). We see siRNAs with smaller Dif_5–3 values are more likely to be predicted as active and the converse for siRNAs with higher Dif_5–3 values.

Painting a more detailed picture: telling the story of active siRNAs

What insights about active siRNAs can we gain from the model and shown plots? We see from the response 1D plot above that a more negative Dif_5–3 value is indicative of active siRNAs. We know that this feature represents the binding strength at the 3'-end of the guide strand minus the binding strength at the 5'-end of the guide strand. We also know that if binding is more tight it will have a larger negative ∆G value. Therefore the preference we see of a smaller (more negative) Dif_5–3 value entails that active siRNA have a loosely bound 5'-end and tightly bound 3'-end (larger negative value of 3'-∆G — smaller negative value of 5'-∆G = relatively larger negative Dif_5–3 value). The double negatives here can be tricky. Here’s an image to wrap your head around what we mean.

Tight binding in active siRNA
Combination of tight binding at the 3’ end and loose binding at the 5’ end leads to the large negative value of Dif_5–3 seen in active siRNA.

In addition, we know that position 1 is at the 5'-end of the guide strand and position 19 is the 3'-end. It is also known that GC-rich sequences lead to tighter binding and AU-rich sequences lead to looser binding. Therefore, from Dif_5–3 we expect that A and U at position 1 are favorable since it would lead to loose binding at the 5' end. This is exactly what we see with the categorical weights ranking U and A as the most favorable and G and C as the least preferred at position 1.

Essentially the model has pointed two fingers at the importance of a large difference in the binding tightnesses at the two ends of the siRNA for activity. Directly by including Dif_5–3 and indirectly by pointing to position 1 — the 5' end of the siRNA where dinucleotide content leads to tight or loose binding — as important.

Digging deeper

In fact, it is dinucleotide content at the two ends of the strand that really leads to dramatic differences in binding affinities, not simply singular nucleotides. So the statement that U and A is preferred at position 1 because it leads to looser binding at the 5' end is not an incorrect statement, but it doesn’t capture the whole picture. Yes, U or A at the first position is more favorable, but this is because A/U-rich dinucleotides (AA, AU, UA, UU) are more favorable. Similarly, G and C at the first position are still unfavorable, but because G/C-rich dinucleotides (GG, GC, CG, CC) are unfavorable.

You shouldn’t just trust this statement. We can test this claim by introducing positional dinucleotide features to the data. Think of this as a way of further testing our proposed mechanism where the balance between 3' end and 5' end binding tightnesses is a lead indicator of active siRNA.

Data prep

Again, we’ll train and test on the same data subsets as the researchers. We’ll also perform the same data preparation steps as earlier.

siRNA data set

Finding a model

Abzu QLattice model

As hypothesized, the QLattice has identified that the dinucleotides present at the two ends of the guide strand are important predictors of dinucleotide activity.

Evaluating model performance

Abzu QLattice model

We see that the AUC scores (both on the train and test sets) are higher for this model; we have gained more predictive power by including dinucleotide features. This hints that more information about siRNA activity lies in the dinucleotides present at the beginning and end of the sequence than in the single nucleotides present.

Favorable dinucleotide combinations

Again we can use the categorical weights to determine preferred and avoided dinucleotides at position 1 and 18. Both ‘di1’ and ‘di18‘ are positively associated with class, so the larger the associated weight, the more favorable. In the plots below the dinucleotides are ordered from most to least preferred.

Ordered dinucleotide weights

We see that the combination of A/U-rich dinucleotides at the first position with G/C-rich dinucleotides at the last position is the biggest indication of active siRNA. This is exactly what we expected to see given our previous model and the findings of the researchers.

In summary: An exploratory workflow

Here we have explored how the QLattice can act as a companion in hypothesis-driven exploration. We were able to use our early models as a compass for where to investigate further. From the features we saw in these, we were able to strategically add more interpretable features that captured the same mechanisms. In doing so, we uncovered a significant attribute of active siRNA: having a loosely bound 5’ end and tightly bound 3’ end. Furthermore we’ve described how this can be achieved via specific combinations of nucleotides at the two ends of the siRNA. We could’ve stopped after the initial simple model, but with limited understanding of its features, it would be difficult to draw the same conclusions and understandings. What a shame that would be!

Horizontal rule

This piece wouldn’t have been possible without Lykke Pedersen & Meera Machado

References

Ichihara, M., Murakumo, Y., Masuda, A., Matsuura, T., Asai, N., Jijiwa, M., Ishida, M., Shinmi, J., Yatsuya, H., Qiao, S., Takahashi, M., & Ohno, K. (2007). Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic acids research35(18), e123. https://doi.org/10.1093/nar/gkm699NLM

Shabalina, S. A., Spiridonov, A. N., & Ogurtsov, A. Y. (2006). Computational models with thermodynamic and composition features improve siRNA design. BMC bioinformatics7, 65. https://doi.org/10.1186/1471-2105-7-65

Contributors

  • Liv Toft, Intern

    Liv is our awesome intern. She rocks our socks by playing with QLattices, coding notebooks on Kaggle, and creating visuals and content. She likes running (slowly) and generally doing anything outside, or treasure hunting in second-hand stores. She looks fly in any of her many pink blazers.

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